In [1]:
%matplotlib inline
def iffie_innie(x1,y1,x2,y2,max_x, max_y)¶
def iffie_innie(x1,y1,x2,y2,max_x, max_y):
""" determine if the box is within the image
"""
if x1 > 0 and y1 > 0 and x2 < max_x and y2 < max_y:
return True
else:
return False
In [2]:
import time
nb_start_time = time.time()
import os
import tempfile
import sys
from collections import OrderedDict
import argparse
import tensorflow as tf
from tensorflow import io as tf_io
import numpy as np
import pandas as pd
import yaml
from skimage.filters import threshold_otsu
from skimage.color import rgb2lab
from PIL import ImageDraw
from PIL import TiffImagePlugin as tip
import IPython.display as ip_display
import openslide
sys.path.insert(0, '../src/python')
from digipath_toolkit import *
def iffie_innie(x1,y1,x2,y2,max_x, max_y):
""" Usage: True_False = iffie_innie(x1, y1, x2, y2, max_x, max_y)
determine if the box is within the image
"""
if x1 > 0 and y1 > 0 and x2 < max_x and y2 < max_y:
return True
else:
return False
def im_pair_hori(im_0, im_1):
""" Usage: new_im = im_pair_hori(im_0, im_1)
combine a list of PIL images horizontaly
"""
w0 = im_0.size[0]
w = w0 + im_1.size[0] + 1
h = max(im_0.size[1], im_1.size[1])
new_im = tip.Image.new('RGB', (w, h) )
box = (0, 0, w0, h)
new_im.paste(im_0, box)
box = (w0+1, 0, w, h)
new_im.paste(im_1, box)
return new_im
In [3]:
test_data_dir = '../../DigiPath_MLTK_data/RegistrationDevData/'
os.listdir(test_data_dir)
offset_data_file = os.path.join(test_data_dir, 'wsi_pair_sample.csv')
if os.path.isfile(offset_data_file):
offset_df = pd.read_csv(offset_data_file)
offset_x = offset_df['truth_offset_x'].iloc[0]
offset_y = offset_df['truth_offset_y'].iloc[0]
offset_x, offset_y = int(round(offset_x)), int(round(offset_y))
auto_x = offset_df['auto_offset_x'].iloc[0]
auto_y = offset_df['auto_offset_y'].iloc[0]
auto_x, auto_y = int(round(auto_x)), int(round(auto_y))
print('\noffset_x, offset_y, auto_x, auto_y\n', offset_x, offset_y, auto_x, auto_y)
fixed_wsi = os.path.join(test_data_dir, '54742d6c5d704efa8f0814456453573a.tiff')
fixed_levels_dict = get_level_sizes_dict(fixed_wsi)
fixed_max_width = fixed_levels_dict['image_size'][0]
fixed_max_height = fixed_levels_dict['image_size'][1]
print('\n\nfixed_wsi image: 54742d6c5d704efa8f0814456453573a.tiff')
for k, v in fixed_levels_dict.items():
print('%25s: %s'%(k,v))
float_wsi = os.path.join(test_data_dir, 'e39a8d60a56844d695e9579bce8f0335.tiff')
float_levels_dict = get_level_sizes_dict(float_wsi)
float_max_width = float_levels_dict['image_size'][0]
float_max_height = float_levels_dict['image_size'][1]
print('\n\nfloat_wsi image: e39a8d60a56844d695e9579bce8f0335.tiff')
for k, v in float_levels_dict.items():
print('%25s: %s'%(k,v))
In [4]:
try:
wsi_obj_0.close()
except:
print('wsi_obj_0 object De Nada')
In [14]:
run_parameters = {'wsi_filename': fixed_wsi,
'wsi_floatname': float_wsi,
'thumbnail_divisor': 20,
'patch_select_method': 'threshold_rgb2lab',
'rgb2lab_threshold': 80,
'image_level': 0,
'patch_height': 224,
'patch_width': 224,
'threshold': 0,
'offset_x': offset_x,
'offset_y': offset_y}
patch_igetor = PatchImageGenerator(run_parameters)
wsi_obj_0 = openslide.OpenSlide(run_parameters['wsi_floatname'])
In [15]:
n_2_try = 100
print('offset_x ', run_parameters['offset_x'], '\t', 'offset_y ', run_parameters['offset_y'], '\n')
for _ in range(n_2_try):
nptch_dict = patch_igetor.next_patch()
fxd_im = nptch_dict['patch_image']
image_level = run_parameters['image_level']
patch_size = (run_parameters['patch_width'], run_parameters['patch_height'])
x1 = nptch_dict['level_0_x'] - run_parameters['offset_x']
x2 = x1 + run_parameters['patch_width']
y1 = nptch_dict['level_0_y'] - run_parameters['offset_y']
y2 = y1 + run_parameters['patch_height']
print('fixed_x: %i float_x: %i\tfixed_y: %i float_y: %i'%(nptch_dict['level_0_x'], x1,
nptch_dict['level_0_y'], y1))
if iffie_innie(x1, y1, x2, y2, float_max_width, float_max_height) == True:
flot_im = wsi_obj_0.read_region((x1, y1), image_level, patch_size)
display(im_pair_hori(fxd_im, flot_im))
else:
print('out of bounds')
In [16]:
try:
wsi_obj_0.close()
except:
print('wsi_obj_0 object De Nada')
In [ ]: